Atomic Vision.(Company Business and Marketing)

A new volume rendering tool sheds light on molecular activity

Atoms and molecules never looked so good, thanks to a novel visualization technique developed at NASA Ames Research Center. Called EVolVis, for electronic volume visualizer, the software lets scientists see atomic and molecular structures and interactions in a way never before possible by computing and visualizing the mathematical properties of the electrical charge distributions of the structures.

The tool addresses one of the major drawbacks of existing molecular visualization approaches, says Preston MacDougall, a chemistry professor at Middle Tennessee State University and collaborator on the research project with NASA Ames visualization expert Chris Henze. The majority of current techniques, he says, "do not visualize atoms in molecules with dutiful attention to the fact that real atoms interact with each other quantum mechanically."

For example, many of the rule-based molecular visualization algorithms rely on an averaging approach to approximate distinctive features in a dataset. Unfortunately, says MacDougall, "the molecular interactions that are the least understood are those that are described as weak and noncovalent." Such interactions are often averaged into non-existence using current methods. In contrast, EVolVis lets users identify and explore subtle interactions--the "lumps and holes" most approaches miss, says MacDougall--by focusing on local concentrations of electron density rather than properties derived from global integration.

The property being considered maps regions of local charge concentration and local charge depletion in a molecule. This property is called the Laplacian of the total electronic charge density. By unveiling the topology of the Laplacian specifically, EVolVis uncovers variations that characterize reactive sites in molecules--information that is then visualized for interactive exploration.

The software relies on volume-based rather than surface rendering techniques, which means that users can probe entire molecules without obstruction by opaque surfaces and without having to preselect specific views or layers. The information attained from such a holistic perspective provides critical clues into molecular behavior, including why molecules take their distinctive shapes, how they orient themselves for chemical reactions, and even where new atoms may bind if a molecule is bent out of shape.

Molecular Data Mining